TMNT of SHIELD
by robert32514
Summary: Raised by S.H.I.E.L.D. and taught in the ways of their fallen father, The Teenage Mutant Ninja Turtles will rise to the challenge and face their destiny head on with Nick Fury, Phil Coulson, Maria Hill, and the Avengers on their side. Based on a combination of new the movie and original animated version.
1. Chapter 1

**TMNT of S.H.I.E.L.D.**

**Prologue**

**I do not own TMNT or Avengers**

**Peter Laird, Kevin Eastman, and Marvel do.**

**Positive Reviews are welcome.**

** Prologue**

** June 11, 1997 8:27 Pm**

** S.H.I.E.L.D. Triskelion**

Nicolas Fury, Director of S.H.I.E.L.D. was staring out of his office window as construction of the very first Flying Battleship or Heli-Carrier ever was in the beginning processes of being built below S.H.I.E.L.D.'s main base of operations. He was contemplating his career and the path it was on when a noise within his office drew his attention. Drawing his service revolver upon turning to the source of the noise, he looked with his one good eye as a somewhat small unknown humanoid presence in a dark robe that covered it almost completely minus its snout as the only sign of it being anything close to human was a wet black nose. On its back was what appeared to be a huge bag-like object that appeared to be moving. He was drawn out of his curiosity when a familiar voice called out his name from underneath the dark cloak that now appeared to be leaking what looked like blood, "Fury-son!"

The humanoid being then fell forward to the floor with the bag falling to its left side. Fury knew the voice under the hood as he quickly rounded the desk and fell to his knees. "Yoshi, can you here me, Yoshi." He pulled the apparent body of Hamato Yoshi around and slightly lifted him into his arms as the hood dropped and Nicolas Fury got the biggest shock of his life as he gazed at the now unfamiliar visage of his longtime friend who seemed to now be a humanoid rat, "F..Fury-son, my f-friend. No-not much...time..."

"Yoshi, who did this to you?" Nick looked at the body of his friend as his robe's was torn with splashes of blood as it was pooling around the body.

"Mu-Mutagen. Was exposed...to Mutagen. Hid under...underground for a-a time." The mutated rat form of Hamato Yoshi managed to gasp out as he then turned to the still slightly moving bag next to him, "Protect...Protect my sons...Protect them from Saki."

"Saki? Oruku Saki? Is he the one who is after you and did this to you?" Fury demanded as he looked upon his mutated friend who sported many cuts and stab marks. His friends breathing then began to become worse. Yoshi could only nod as his eyes never left the bag.

"Leonardo, Donatello,...Mi...Michelangelo, Raph...Raphael. That is their names. Raise them well...my friend. Have them trained...in my ancestors..."

Fury shook his head no as he quickly pulled out a communications device and was calling for a medic as Yoshi was willing his sons to Fury. "You're going to train them yourself, old friend. You're their father."

With the last of his strength, Hamato Yoshi grabbed the hand that was on his chest and gave one last smile and said, "You...are their...father now...old friend."As he drew his last breath, he felt the fluids now flowing in his lungs as with a final sigh, his left hand fell, and he was gone.

Seeing the sight of his friend dead not even a second, in his arms, Fury called out, "Yoshi,...YOSHI, DAMN YOU... **YOSHI!"** he cried out as he gently shook his friends body to helplessly will him to come back.

The medics came yet paused as they were startled upon gazing at a mutated humanoid rat in their bosses arms until Fury demanded they do what they were called to do and try and bring Yoshi back as his eyes landed on the bag that began moving even more and held sounds like newborn babies. The mutated body of Hamato Yoshi was placed on a girder and quickly wheeled off to the emergency room to try and save him if they could. Nicolas then heard crying coming from the bag as he took a chance and slowly opened it and jumped back in shock as his eyes landed on four baby humanoid turtles, at the natural size of normal human babies.

Of the Agents that remained behind was an Agent named Philip Coulson who gasped in shock as he too looked upon the infant humanoid baby turtles. Nick Fury came closer and saw what appeared to be metal beaded wrist bands with the Turtles names in color coded amulets, blue for Leonardo, red for Raphael, purple for Donatello, and orange for Michelangelo.

The four orphaned infant turtles looked at their surroundings and then upon the men who now knelt before them to look upon them as they had looks of shock that was replaced with fear, and then crying as they held onto one another. Phil took the initiative to sooth their crying as a beep came through and Fury took the call from the communication device on his belt. A moment later, Fury asked the Agent to watch over the children until his return. An hour later and Fury returned to find Phil Coulson on the floor with the baby turtles curled up together in his arms and lap, fast asleep. Coulson turned to gaze upon his boss who took one look and lowered his head to the floor and shook it. Coulson knew what that meant as he felt for the little guys.

"Boss, what are we gonna do?"

"Yoshi's last wish was they be trained in the way of his ancestors." He said as he pulled a bottle of Bourbon and a set of glasses for himself and Coulson. Pouring for both of them, he held one out as He explained what Yoshi had told him, especially about something called Mutagen and what it did to him and the baby turtles and the one who killed him. Fury then decided to personally see to the death of Oruku Saki himself, but his first order of business would be to the welfare of the babies in his Agents arms. He then explained that that meant they were trained to be Ninja's as Yoshi's family was in fact documented to have descended from an ancient warrior Clan of Ninja, who were of an honorable family.

"You sure that's wise boss? I mean, their just babies!" Coulson said as he quickly downed the drink in one shot after hearing the explanation.

Fury nodded solemnly as he looked at Coulson with his one good eye, "It's what he wanted."

"And Saki?"

"For now, we wait and observe him from a distance. His time's coming, and when it does, if the Turtles don't kill him, I will." Fury said darkly as he began to plan and set into motion a chain of events that would change the course of world history forever.

**Read and loved Leofan221 Turtle/Avenger crossover despite the time difference that didn't necessarily make any sense, but still loved it nonetheless. So, this is my version that will be corresponding with the Avengers films. I also personally own copies of both Movies as well as the original '1990s' films. So read, review, and let me know what you think. Until Next Time.**


	2. Chapter 2 Like Shadows in the Night

**TMNT of S.H.I.E.L.D.**

**Ch.1 Like Shadows in the night.**

**I do not own TMNT or Avengers.**

**Peter Laird, Kevin Eastman, and Marvel do.**

**Positive reviews are welcome.**

** Ch. 1 Like Shadows in the night.**

** New York, New York**

** March 17th, 2012**

** 9:18 pm**

** Bay Harbor**

A Security Officer at of the New York harbor was doing his nightly rounds when he came upon several men who were breaking into a crate and unloading what looked to be serious high-tech weapons and placing them into their vehicles. The second he came upon the scene, he hid behind one of the crates next to the one that was now being emptied. He did not know he was seen until he felt what seemed to be a throwing star one only seen in movies as it flew past his left cheek and stuck to the crate with a metal _'twang'_, lightly nicking his right cheek. He brought his right hand up and felt the cut and fresh blood now flowing down the side of his face. His heart rate sped up as he began to run, not caring where or seeing the shadows of dark clothed men in Ninja clothing with what looked like swords strapped to their backs, chasing him from behind and above. He only managed to see one of them who ran ahead of him on top of another crate as he felt a pain in his right ankle that forced him to fall to the ground and slide forward until his head hit another crate, realizing that he unintentionally ran into a dark dead end.

He backed up as best he could as he saw he was surrounded by what appeared to be Ninja's and then gazed at his right leg and found a metal throwing star buried in his ankle. The lights didn't hide the shadow warriors as they closed in on the defenseless officer, until suddenly the lights sparked and exploded out completely in the surrounding area as the last thing he saw was the ninja clad assassins as they looked up and around as the darkness fell.

Suddenly from within the darkness, sounds of thumps were heard alongside screams of pain and bodies hitting pavement. There was even the occasional sounds of mocking comments that sounded like a surfer accent seen and heard in movies, as well as another with the accent of someone from Boston. There were even sounds that sounded strangely like metal on metal as well as chains and wood spinning as one.

The officer didn't know how long he was there when the sounds stopped as he felt the release of the pain that his ankle was under as someone must have removed the throwing star. He felt like he could walk on clouds moments later until a light hit him in the face as police lights from two different directions came upon him. The lights then fell on the Ninja clad beings who appeared to be tied up with both ropes and chains. His ankle was bandaged and seen to by whoever his savior was.

Hours later, the whole of new York would know of the discovery of the black clad Ninja's and the high-tech weaponry found in the crate as well as the Harbors Security Officer who was attacked by what appeared to be real life Ninja's that were somehow overtaken by another group of unknown fighters when the lights went out as they even went so far as to render first aid to the said Officer. The Ninja's, though unconscious were rounded up, disarmed completely, and stuffed into caged vehicles that would see to their incarceration.

Nick Fury was watching the news of the nights events with a smile on his face as he watched the news feed from his laptop as he was riding in the passenger seat of a standard unmarked S.H.I.E.L.D. vehicle with Agent Phil Coulson driving, and Maria Hill as a passenger, heading to the hidden base where he would meet up with his adopted Nephews. Though he loved them as his sons, he knew he could never replace Hamato Yoshi. The hidden base was a former underground railway system that now served as one of many hidden S.H.I.E.L.D. bases that now served as his nephews home. A tunnel was made that allowed Nick and anyone he chose to allow access to follow him as the road opened from an undisclosed location in an alleyway of New York, and traveled down as Coulson followed his memory on where to go.

"Sir are you sure it's necessary to allow them to join us for this mission?" Maria Hill asked as she didn't like using her pseudo brothers in such a way. She was shocked when she first found out about the Turtles, but soon came to love them as she got to know them. They were innocent, well almost innocent. Raphael was a hothead warrior, Leonardo a natural born leader, Donatello was a science geek and one of the worlds leading tech experts though hidden as he was, and Michelangelo, her baby brother Mikey, he was the heart and soul of the team as well as world class prankster at heart. She'd give anything to see to their safety. "I mean, their still teenagers."

"Yet they are bigger, stronger, and faster than most ordinary world class human bodybuilders with the skills to put even the most accomplished Ninja to shame as you are undoubtedly seen of the news tonight, Hill. They're ready. And with Loki's arrival, and the Tesseract gone, we're going to need every available person we can muster."

"Phil, help me out here." Hill pleaded looking to her fellow Agent and friend.

"Sorry Hill, I'm with Fury on this one. Besides, the boys are getting restless having to hide all the time. I think them working alongside those we've slotted for the Avengers Initiative will be a good thing and allow them to unwind a bit. Like Fury said, they're ready. Besides, we also have to debrief them about tonights Ninja attack at the Bay Harbor."

They stopped before a wall that seemed to be a dead end until two brick-like objects within both side appeared from the brick and concrete walls. They looked like normal bricks that were being pushed by a metal pole until they split apart revealing a retinal scanner, thumbprint scanner, and a voice box as both Fury and Coulson looked into the retina scanners and placed their thumbs on the thumb print scanners and spoke, "Fury, Nicolas J." and "Coulson, Philip".

The objects did their scans after verifying the identities of the car passengers and then were pulled back into the walls. The front wall then seperated, bathing the vehicle in yellow light as the vehicual garage area of the Turtles home welcomed the new arrivals as it opened, the Agents and Director gazed upon the home of the Teenage Mutant Ninja Turtles. It had everything the Turtles needed besides a set of two Train Carts for homes, a Training facility, Skating Rink, Computer Station, a Kitchen, Dining Room, and A game room. There was even a Garage where the Boys tech's expert Donatello, appeared to be under the new vehicle, putting his mechanic and tech savvy skills to work in giving the Turtles the necessary edge in motive transport. Raphael was currently punching a large sandbag that was quadrupled in size for a guy with his immense strength and attitude. Leonardo was currently kneeling and meditating before a burning incense that was in front of a picture of Hamato Yoshi, while Michelangelo was playing video games.

It was Leo that had the Turtles look up from what they were doing as the Diretor and agents exited the vehicle and came forward, "Uncle, is everything alright?" Leonardo was dressed in padded gear, a blue bandanna mask, and several articles or items that led others to think of Leo as a Samurai more than anything as he carried two Katana Swords strapped to his back in a criss cross pattern. Raphael stopped pounding the Sandbag as his giant musculature bulk would have people fleeing in terror since he put off an aura with an offensive attitude. Raphael was prone to anger issues as was the normal for him. Like his brothers, he too wore a bandanna, but was red that covered his entire head, with a variety of things all over him from burnt brands of Japanese characters to tattoos of Hawaiian tribal symbols. He also had tape on his outer shell due to cracks here and there due to past training accidents and fight incidents between he and Leo, and a set of glasses on top of his mask. A set of huge Sai's sheathed on either side of his waists.

Donatello, walked from underneath the walk-in area under the new Turtle Van with a rag in his hand as he just cleaned his hands of the engine oil and grease. He had a purple bandanna with taped glasses over them, a set of tech devices on both arms, chest, and even a computer on his outer shell. He had a set of infra-red goggles on his forehead, and even a camera device on his left shoulder. Under the computer behind his back was an extendable Bo-staff that was able to extend and shrink at the press of a button, and could withstand a great amount of pressure. Unlike his other three siblings, though Donatello was strong, he wasn't stacked like Raph or Mikey, but was somewhat physically built close to how Leo is. He nodded at his pseudo Uncles and adopted sister as he walked up.

Michelangelo quickly dropped his game controller and hopped over the couch he sat on and rushed up to Maria and picked her up in his hands and twirled her around, much to her enjoyment. "MARIA, you're here. You're really here. Did you bring me anything?" Mikey asked excitedly. Like Raph and Leo, Mikey was well built, though Donny was taller and leaner, Mikeys hands were bandaged up in white wrapping, as he also wore miniature sea shells as a necklace, white glasses, and an orange bandanna. Hanging on either side of his wastes was his Nun-chukus and on his outer shell was a specialized skate board made just for him, thanks to Donatello. It could shoot him off like a rocket when he wanted to go somewhere or hop over buildings and such that couldn't normally be reachable.

"Easy Mikey, and yes I did." Maria laughed as he set her down so she could walk back to the car and pulled out his favorite Meat-Lovers Pizza, of which she bought several boxes of different pizzas, due to the Turtles huge taste differences, huge bodies, and their huge appetites.

"What's up Fury? Uncle Phil?" Raph asked grumpily.

"We got ourselves a situation, and I think you four could be a part of the solution. But it means coming out in the open and possibly letting that scumbag Saki know your still alive." Fury said as he gazed at all four of his boys.

Raph growled at that as he pulled out both Sai's and twirling them in his three fingered hands before sheathing one of them again. The other in his left hand was held up, "If he shows up, I'm putting both of these in his eyes." He said as he twirled it again and placed it in the left sheath. Leo just shook his head at Raph's current attituda as it didn't do much to get his brother riled up.

Fury nodded as the Turtles and Agents went into the dining room and sat at a table as Fury pulled out a computerized holo-file. Donatello pulled it to him and set to work in using it to bring up the information as Mikey with a slice in his hand paused as he looked at his and Leo's favorite Hero of all time, Captain America. Fury used to tell the turtles stories about the First Avenger when they were young. The information that the Turtles were permitted to know through the computer was that he had been found near the Arctic and retrieved, as well as was part of the Avengers Initiative, which Leo and Donny thought was shut down.

Then Mikey was dealt a blow to his heart when he found out how the God he worshiped for years had actually showed up at one of the secret S.H.I.E.L.D. installations and killed a lot of S.H.I.E.L.D. Agents in less than two days. It was when Raph looked at Maria and saw the still healing cut on her head that made him want to tear Loki apart. "Man, that's harsh, over 80...people man." Mikey said after he lowered his slice of Pizza and lowered his head in silence for the people killed by Loki. His brothers did the same in respect to the victims of Loki's actions.

Raph and Leo looked at one another and nodded as both came to the same conclusion as Leo looked at the Director, "When do you need us Uncle Nick?" For the remainder of the night, as the Director, Agents, and Turtles ate, they also discussed the recent events and the discovery that Saki was indeed back as Donatello found a medallion on one of the Ninja's that showed Saki's mark of a three pronged foot-like symbol in red on a silver coin-like medallion. For the next two days, they planned, as for tonight and the next day after, they would mentally and physically prepare themselves, for when the ride to the main meeting point would land them on the first ever Heli-Carrier. They would get a chance to meet some of the names that was also on the Avengers Initiative, as they were.

After the second day, they were ready as they were armed and prepped, but the moment they were out of the lair, they had to hide their identities under hooded cloaks until they got to the Carrier. A good portion on the deck crew were curious and weirded out at seeing four huge and bulky beings in dark hooded cloaks being led to the inside of the ship by S.H.I.E.L.D. Agents, and driected to the bridge. Once inside, Fury met them at the entrance and directed them to a room where Captain Steve Rogers, Bruce Banner, and even Natasha Romanoff were in the middle of watching the Turtles complete history. Once it was over, the turtles were allowed to drop their hoods.

Michelangelo though could not contain himself and automatically ran to and knelt in front of the Captain as if to worship him, much to his brothers ire as he repeated time and time again "I'm not worthy!"

"Awe, come on Mikey, get off the floor. Stop pestering the man." Raph said as he stuck a toothpick in his mouth.

"Mikey, did we not say we would not worship the Captain as he isn't a God. He's mortal, just like you." Leo shot out as he watched as the Captain grin shyly.

"Th..They can talk!" Bruce Banner stuttered in astonishment.

"I think that's already been confirmed through the video, Bruce." Natasha replied with a smirk as Leo and the Captain stepped up to one another and shook hands.

"I'm Leonardo, team leader, these are my brothers, Raphael the muscles and brawn of our group in red," Raph nodded slightly as he only glowered and crossed his arms in slight agitation. He leaned on a wall near a corner watching the introductions. He really wanted to see some action. "Donatello the genius of the family in purple," Donny had already discarded his robe unlike the others as he sought to shake Doctor Banners hand and begun to talk in the language of Science that almost no one within the room, save those two, understood. Doctor Banner was really intrigued with the intelligence all the turtles had, but even more so with Donatello and the amount of self made tech Donny had all over his person "And of course the baby of the family as well as heart, soul, and all around prankster of our team in orange, Michelangelo." Mikey was jumping up and down in giddiness as he then shook the Captains hand with both of his hands, "Dude, you're like, the greatest legend ever." Michelangelo said as Fury silently chuckled while hiding his face at Michelangelo's antics as Leonardo continued, "It will be an honor working with you Captain, Uncle Nick and Uncle Phil has spoken very highly of you and I may have used it as another reason why I where blue, somewhat." he chuckled. "You've been an inspiration to our countries history, and I hope we can only dream of following your example." Leo finished as he stepped back and bowed, to which his brothers followed, though Raph was hesitant at first until Leo smacked him on the chest with the back of his hand.

"Uh,...thanks!" Steve said with nervousness in his voice as he returned the show of respect and bowed back.

"Donatello, you'll be working beside Bruce in trying to locate the Tesseract." Fury said as he looked at his purple masked tech-specialist nephew who nodded in understanding.

The remaining turtles disrobed and walked to the main bridge with Fury and the other Agents and Captain Rogers as the ship was undergoing the steps to vanish through retro reflective panels. The turtles noticed that their adopted sister Maria Hill was just finishing with the proper protocols before liftoff.

It all of a sudden got quiet on the bridge as everyone minus those in the know looked at the Turtles in shock until Fury looked around and demanded the workers to get back to work at their stations and to mind their stations instead of minding the Turtles.

It was when Banner asked where Fury was on the recovery of the Tesseract that Bruce informed him to call every lab he and S.H.I.E.L.D. knew to put their Spectrometers on the roof and Calibrate them for Gamma rays. Donny input his own thoughts as he replied that he and Dr. Banners would rough out a tracking algorithm basic cluster recognition to at least rule out a few places.

"Do you have anywhere for me and Donatello here to work?" Bruce asked as he began curling his violet shirt sleeves up his arm.

"Agent Romanov, would you be so kind as to escort Dr. Banner and Donatello to their Laboratory, please?" Director Fury asked of his red headed Agent.

She stood from where she sat and nodded. She gestured for the scientist and purple masked turtle to follow her, "Right this way gentlemen, You're gonna love it. We have all the cool toys."

As Leonardo stood by Nick and watched as he took charge, he watched as Mikey acted like the child he sometimes could be as he went up to and looked out the view-port of the Heli-carrier in amazement. Raphael meanwhile just stood stone still while chewing on his toothpick. He was beginning to lose his patience after having seen the computer packet reveal the death toll caused by Loki upon his arrival and at his hands. Leonardo saw this and placed a hand on Raph's left shoulder, "Don't worry, Uncle Nick has assured me that you, Mikey, The Captain, and I will act the moment he surfaces. Donnie's sticking with Banner until they can manage to track the cube."

Raph didn't need to know who he was that his older brother was referring to. He saw multiple people sneaking glances upon him and his brother and he could honestly say, he wasn't happy being looked at like a freak.

Fury saw the looks people were giving his adopted nephews and hollered out at the ones doing the gawking as he raised his voice so everyone heard him as he looked around the bridge, "Anybody got a staring problem. Eye's on your station people, not my nephews. I catch one person looking at them wrong, and I'll have your ass fired faster than you can blink. Any sudden pictures snapped of them, and I'll throw your asses off the ship myself. Now, get back to work."

Not one person disobeyed his order as the staring stopped. It was then that Agent Sitwell, a tan skinned, young agent with a bald head and glasses had shot out a possible sighting of the asgardian Loki in Germany as a cell phone cam caught Loki looking around and smirking as if expecting someone to stop him. Leo, having studied under Fury's tutelage on reading body languages was the one who spoke next.

"I don't like this. It was too easy, and it's like he's waiting for you and daring you to come for him, Uncle."

"Then let's not disappoint him. Captain, you're up. Leo, you'll follow the Captains lead. Raph and Mikey will follow yours. Please, don't screw this up with your hot headedness Raphael." the Director said, tilting his head to gaze upon his nephew with his one eye. Raph just growled in annoyance again as he quickly snatched his Sai's from where they were sheathed, twirled them extremely fast in between his three fingers in both hands, and sheathed them again in less than five seconds, anticipating the chance to finally see some action and test out just how much a God the Asgardian really was. He then cracked his knucles and grinned michievously as if to say, "Who, me?"

In twenty minutes, Captain America was being led to a hangar by Agent Coulson with Leonardo, Michelangelo, and Raphael trailing behind as Agent Romanoff and another pilot took their places at the Pilot and Co-Pilot station of one of the Quin Jets. Settling in and strapping down, the jet was given the clearance it needed for takeoff, and flew off into the night to Stuttgart, Germany.

**The turtles in this are designed as they were in the movie, as I loved it much, in the next Chapter, Loki gets the surprise of his life as he sees the Turtles that not even agent barton knew about and receives a can of woop-ass from our favorite red masked turtle. Till next time. **


End file.
